Eu acho que você está experimentando um comportamento "compartilhado", enquanto você precisa de "privado". Consulte man 8 mount
:
The shared subtrees operations.
Since Linux 2.6.15 it is possible to mark a mount and its submounts as shared, private, slave or unbindable. A shared mount provides ability to create mirrors of that mount such that mounts and umounts within any of the mirrors propagate to the other mirror. […] A private mount carries no propagation abilities. […]
Solução: após mount --bind …
e antes de mount -t overlay …
invocar:
sudo mount --make-private /home/username/Store/Orig/usr